srst2 0.2.0-foss-2018b-Python-2.7.15

Deprecated: Use of this version of srst2 is deprecated. More information on our Applications Support and Retention Policy.

Short Read Sequence Typing for Bacterial Pathogens. This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

Accessing srst2 0.2.0-foss-2018b-Python-2.7.15

To load the module for srst2 0.2.0-foss-2018b-Python-2.7.15 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load srst2/0.2.0-foss-2018b-Python-2.7.15

BEAR Apps Version

2018b

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

More Information

For more information visit the srst2 website.

Dependencies

This version of srst2 has a direct dependency on: Bowtie2/2.3.4.2-foss-2018b foss/2018b Python/2.7.15-foss-2018b SAMtools/0.1.18-foss-2018b

Last modified on 5th June 2019